Script not working in Galaxy - galaxy-dev

22 Jun 2012


      Hi all,
I have integrated a script that runs rsem in Galaxy and the following is
the .xml that shows it in Galaxy:
<tool id="sixthStep" name="RESM">
 <description></description>
 <command interpreter="perl">exec_rrsem.pl $input1 $input2 $input3 $output1
$output2
 </command>
 <inputs>
  <param name="input1" format="fasta" type="data" label="Transcript from
OASES"/>
  <param name="input2" format="fastq" type="data" label="Left read: " />
  <param name="input3" format="fastq" type="data" label="Right read: "/>
 </inputs>
 <outputs>
  <data name="output1" format="text" />
  <data name="output2" format="text" />
 </outputs>
</tool>
And here is exec_rrsem.pl, the file that accepts the parameters and sets
everything up:
$genes = $ARGV[3];
$isoforms = $ARGV[4];
$trans = $ARGV[0];
$left = $ARGV[1];
$right = $ARGV[2];
$directory = "/home/applications/galaxy-dist/tools/VELVET-OASES";
$transcript = "$directory/trans.fa";
$left_read = "$directory/left_read.fastq";
$right_read = "$directory/right_read.fastq";
symlink $trans, $transcript;
symlink $left, $left_read;
symlink $right, $right_read;
@out #@out = `perl /home/applications/galaxy-dist/tools/VELVET-OASES/
run_rsem.pl 2>&1`;
run_rsem.pl is the actual script that runs the rsem programs. I'm wondering
though, why Galaxy isn't executing the command properly. This is the same
pattern I've used in other programs that I've integrated with Galaxy, so it
came as a surprise to me when this one didn't run. Is there something wrong
with my script? By the way, when I run exec_rrsem.pl from the konsole, it
works just fine. Any insights on this?
Thanks a lot!
CL